1
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Crystal structures of FNIP/FGxxFN motif-containing leucine-rich repeat proteins. Sci Rep 2022; 12:16430. [PMID: 36180492 PMCID: PMC9525666 DOI: 10.1038/s41598-022-20758-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 09/19/2022] [Indexed: 11/14/2022] Open
Abstract
The Cafeteria roenbergensis virus (Crov), Dictyostelium, and other species encode a large family of leucine-rich repeat (LRR) proteins with FGxxFN motifs. We determined the structures of two of them and observed several unique structural features that set them aside from previously characterized LRR family members. Crov588 comprises 25 regular repeats with a LxxLxFGxxFNQxIxENVLPxx consensus, forming a unique closed circular repeat structure. Novel features include a repositioning of a conserved asparagine at the middle of the repeat, a double phenylalanine spine that generates an alternate core packing arrangement, and a histidine/tyrosine ladder on the concave surface. Crov539 is smaller, comprising 12 repeats of a similar LxxLxFGxxFNQPIExVxW/LPxx consensus and forming an unusual cap-swapped dimer structure. The phenylalanine spine of Crov539 is supplemented with a tryptophan spine, while a hydrophobic isoleucine-rich patch is found on the central concave surface. We present a detailed analysis of the structures of Crov588 and Crov539 and compare them to related repeat proteins and other LRR classes.
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2
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Wu S, Zhou L, Zhou Y, Wang H, Xiao J, Yan S, Wang Y. Diverse and unique viruses discovered in the surface water of the East China Sea. BMC Genomics 2020; 21:441. [PMID: 32590932 PMCID: PMC7318539 DOI: 10.1186/s12864-020-06861-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 06/22/2020] [Indexed: 11/23/2022] Open
Abstract
Background Viruses are the most abundant biological entities on earth and play import roles in marine biogeochemical cycles. Here, viral communities in the surface water of the East China Sea (ECS) were collected from three representative regions of Yangshan Harbor (YSH), Gouqi Island (GQI), and the Yangtze River Estuary (YRE) and explored primarily through epifluorescence microscopy (EM), transmission electron microscopy (TEM), and metagenomics analysis. Results The virus-like particles (VLPs) in the surface water of the ECS were measured to be 106 to 107 VLPs/ml. Most of the isolated viral particles possessed a head-and-tail structure, but VLPs with unique morphotypes that had never before been observed in the realm of viruses were also found. The sequences related to known viruses in GenBank accounted for 21.1–22.8% of the viromic datasets from YSH, GQI, and YRE. In total, 1029 viral species were identified in the surface waters of the ECS. Among them, tailed phages turn out to make up the majority of viral communities, however a small number of Phycodnaviridae or Mimiviridae related sequences were also detected. The diversity of viruses did not appear to be a big difference among these three aquatic environments but their relative abundance was geographically variable. For example, the Pelagibacter phage HTVC010P accounted for 50.4% of the identified viral species in GQI, but only 9.1% in YSH and 11.7% in YRE. Sequences, almost identical to those of uncultured marine thaumarchaeal dsDNA viruses and magroviruses that infect Marine Group II Euryarchaeota, were confidently detected in the ECS viromes. The predominant classes of virome ORFs with functional annotations that were found were those involved in viral biogenesis. Virus-host connections, inferred from CRISPR spacer-protospacer mapping, implied newly discovered infection relationships in response to arms race between them. Conclusions Together, both identified viruses and unknown viral assemblages observed in this study were indicative of the complex viral community composition found in the ECS. This finding fills a major gap in the dark world of oceanic viruses of China and additionally contributes to the better understanding of global marine viral diversity, composition, and distribution.
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Affiliation(s)
- Shuang Wu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Liang Zhou
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yifan Zhou
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Hongming Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Jinzhou Xiao
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Shuling Yan
- Institute of Biochemistry and Molecular Cell Biology, University of Göttingen, Göttingen, Germany
| | - Yongjie Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China. .,Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China.
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3
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Degenerate PCR Primers to Reveal the Diversity of Giant Viruses in Coastal Waters. Viruses 2018; 10:v10090496. [PMID: 30217078 PMCID: PMC6163766 DOI: 10.3390/v10090496] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 09/12/2018] [Accepted: 09/12/2018] [Indexed: 01/07/2023] Open
Abstract
“Megaviridae” is a proposed family of giant viruses infecting unicellular eukaryotes. These viruses are ubiquitous in the sea and have impact on marine microbial community structure and dynamics through their lytic infection cycle. However, their diversity and biogeography have been poorly characterized due to the scarce detection of Megaviridae sequences in metagenomes, as well as the limitation of reference sequences used to design specific primers for this viral group. Here, we propose a set of 82 degenerated primers (referred to as MEGAPRIMER), targeting DNA polymerase genes (polBs) of Megaviridae. MEGAPRIMER was designed based on 921 Megaviridae polBs from sequenced genomes and metagenomes. By applying this primer set to environmental DNA meta-barcoding of a coastal seawater sample, we report 5595 non-singleton operational taxonomic units (OTUs) of Megaviridae at 97% nucleotide sequence identity. The majority of the OTUs were found to form diverse clades, which were phylogenetically distantly related to known viruses such as Mimivirus. The Megaviridae OTUs detected in this study outnumber the giant virus OTUs identified in previous individual studies by more than an order of magnitude. Hence, MEGAPRIMER represents a useful tool to study the diversity of Megaviridae at the population level in natural environments.
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4
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Flaviani F, Schroeder DC, Lebret K, Balestreri C, Highfield AC, Schroeder JL, Thorpe SE, Moore K, Pasckiewicz K, Pfaff MC, Rybicki EP. Distinct Oceanic Microbiomes From Viruses to Protists Located Near the Antarctic Circumpolar Current. Front Microbiol 2018; 9:1474. [PMID: 30065704 PMCID: PMC6056678 DOI: 10.3389/fmicb.2018.01474] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 06/13/2018] [Indexed: 12/13/2022] Open
Abstract
Microbes occupy diverse ecological niches and only through recent advances in next generation sequencing technologies have the true microbial diversity been revealed. Furthermore, lack of perceivable marine barriers to genetic dispersal (i.e., mountains or islands) has allowed the speculation that organisms that can be easily transported by currents and therefore proliferate everywhere. That said, ocean currents are now commonly being recognized as barriers for microbial dispersal. Here we analyzed samples collected from a total of six stations, four located in the Indian Ocean, and two in the Southern Ocean. Amplicon sequencing was used to characterize both prokaryotic and eukaryotic plankton communities, while shotgun sequencing was used for the combined environmental DNA (eDNA), microbial eDNA (meDNA), and viral fractions. We found that Cyanobacteria dominated the prokaryotic component in the South-West Indian Ocean, while γ-Proteobacteria dominated the South-East Indian Ocean. A combination of γ- and α-Proteobacteria dominated the Southern Ocean. Alveolates dominated almost exclusively the eukaryotic component, with variation in the ratio of Protoalveolata and Dinoflagellata depending on station. However, an increase in haptophyte relative abundance was observed in the Southern Ocean. Similarly, the viral fraction was dominated by members of the order Caudovirales across all stations; however, a higher presence of nucleocytoplasmic large DNA viruses (mainly chloroviruses and mimiviruses) was observed in the Southern Ocean. To our knowledge, this is the first that a statistical difference in the microbiome (from viruses to protists) between the subtropical Indian and Southern Oceans. We also show that not all phylotypes can be found everywhere, and that meDNA is not a suitable resource for monitoring aquatic microbial diversity.
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Affiliation(s)
- Flavia Flaviani
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa.,Marine Biological Association of the United Kingdom, Citadel Hill, Plymouth, United Kingdom
| | - Declan C Schroeder
- Marine Biological Association of the United Kingdom, Citadel Hill, Plymouth, United Kingdom.,School of Biological Sciences, University of Reading, Reading, United Kingdom.,College of Veterinary Medicine, University of Minnesota Twin Cities, Minneapolis, MN, United States
| | - Karen Lebret
- Marine Biological Association of the United Kingdom, Citadel Hill, Plymouth, United Kingdom.,Limnology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Cecilia Balestreri
- Marine Biological Association of the United Kingdom, Citadel Hill, Plymouth, United Kingdom
| | - Andrea C Highfield
- Marine Biological Association of the United Kingdom, Citadel Hill, Plymouth, United Kingdom
| | - Joanna L Schroeder
- Marine Biological Association of the United Kingdom, Citadel Hill, Plymouth, United Kingdom
| | - Sally E Thorpe
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
| | - Karen Moore
- Exeter Sequencing Service, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Konrad Pasckiewicz
- Exeter Sequencing Service, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Maya C Pfaff
- Department of Environmental Affairs, Oceans and Coasts, Cape Town, South Africa
| | - Edward P Rybicki
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
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5
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Bou Khalil JY, Andreani J, Raoult D, La Scola B. A Rapid Strategy for the Isolation of New Faustoviruses from Environmental Samples Using Vermamoeba vermiformis. J Vis Exp 2016. [PMID: 27341059 DOI: 10.3791/54104] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The isolation of giant viruses is of great interest in this new era of virology, especially since these giant viruses are related to protists. Giant viruses may be potentially pathogenic for many species of protists. They belong to the recently described order of Megavirales. The new lineage Faustovirus that has been isolated from sewage samples is distantly related to the mammalian pathogen African swine fever virus. This virus is also specific to its amoebal host, Vermamoeba vermiformis, a protist common in health care water systems. It is crucial to continue isolating new Faustovirus genotypes in order to enlarge its genotype collection and study its pan-genome. We developed new strategies for the isolation of additional strains by improving the use of antibiotic and antifungal combinations in order to avoid bacterial and fungal contaminations of the amoeba co-culture and favoring the virus multiplication. We also implemented a new starvation medium to maintain V. vermiformis in optimal conditions for viruses co-culture. Finally, we used flow cytometry rather than microscopic observation, which is time-consuming, to detect the cytopathogenic effect. We obtained two isolates from sewage samples, proving the efficiency of this method and thus widening the collection of Faustoviruses, to better understand their environment, host specificity and genetic content.
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Affiliation(s)
- Jacques Yaacoub Bou Khalil
- Faculty of Medicine and Pharmacy, Research Unit for Infectious and Tropical Emerging Diseases, Aix Marseille University
| | - Julien Andreani
- Faculty of Medicine and Pharmacy, Research Unit for Infectious and Tropical Emerging Diseases, Aix Marseille University
| | - Didier Raoult
- Faculty of Medicine and Pharmacy, Research Unit for Infectious and Tropical Emerging Diseases, Aix Marseille University; Pole of Infectious and Tropical Diseases, Clinical and Biological Sector, Federation of Bacteriology-Hygiene Virology, University Hospital Institute Mediterranean Infection
| | - Bernard La Scola
- Faculty of Medicine and Pharmacy, Research Unit for Infectious and Tropical Emerging Diseases, Aix Marseille University; Pole of Infectious and Tropical Diseases, Clinical and Biological Sector, Federation of Bacteriology-Hygiene Virology, University Hospital Institute Mediterranean Infection;
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6
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Giant viruses at the core of microscopic wars with global impacts. Curr Opin Virol 2016; 17:130-137. [DOI: 10.1016/j.coviro.2016.03.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/21/2016] [Accepted: 03/22/2016] [Indexed: 11/21/2022]
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7
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Koonin EV, Krupovic M, Yutin N. Evolution of double-stranded DNA viruses of eukaryotes: from bacteriophages to transposons to giant viruses. Ann N Y Acad Sci 2015; 1341:10-24. [PMID: 25727355 PMCID: PMC4405056 DOI: 10.1111/nyas.12728] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Diverse eukaryotes including animals and protists are hosts to a broad variety of viruses with double-stranded (ds) DNA genomes, from the largest known viruses, such as pandoraviruses and mimiviruses, to tiny polyomaviruses. Recent comparative genomic analyses have revealed many evolutionary connections between dsDNA viruses of eukaryotes, bacteriophages, transposable elements, and linear DNA plasmids. These findings provide an evolutionary scenario that derives several major groups of eukaryotic dsDNA viruses, including the proposed order “Megavirales,” adenoviruses, and virophages from a group of large virus-like transposons known as Polintons (Mavericks). The Polintons have been recently shown to encode two capsid proteins, suggesting that these elements lead a dual lifestyle with both a transposon and a viral phase and should perhaps more appropriately be named polintoviruses. Here, we describe the recently identified evolutionary relationships between bacteriophages of the family Tectiviridae, polintoviruses, adenoviruses, virophages, large and giant DNA viruses of eukaryotes of the proposed order “Megavirales,” and linear mitochondrial and cytoplasmic plasmids. We outline an evolutionary scenario under which the polintoviruses were the first group of eukaryotic dsDNA viruses that evolved from bacteriophages and became the ancestors of most large DNA viruses of eukaryotes and a variety of other selfish elements. Distinct lines of origin are detectable only for herpesviruses (from a different bacteriophage root) and polyoma/papillomaviruses (from single-stranded DNA viruses and ultimately from plasmids). Phylogenomic analysis of giant viruses provides compelling evidence of their independent origins from smaller members of the putative order “Megavirales,” refuting the speculations on the evolution of these viruses from an extinct fourth domain of cellular life.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland
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8
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Andrade KR, Boratto PPVM, Rodrigues FP, Silva LCF, Dornas FP, Pilotto MR, La Scola B, Almeida GMF, Kroon EG, Abrahão JS. Oysters as hot spots for mimivirus isolation. Arch Virol 2014; 160:477-82. [PMID: 25344898 DOI: 10.1007/s00705-014-2257-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 10/11/2014] [Indexed: 11/27/2022]
Abstract
Viruses are ubiquitous organisms, but their role in the ecosystem and their prevalence are still poorly understood. Mimiviruses are extremely complex and large DNA viruses. Although metagenomic studies have suggested that members of the family Mimiviridae are abundant in oceans, there is a lack of information about the association of mimiviruses with marine organisms. In this work, we demonstrate by molecular and virological methods that oysters are excellent sources for mimiviruses isolation. Our data not only provide new information about the biology of these viruses but also raise questions regarding the role of oyster consumption as a putative source of mimivirus infection in humans.
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Affiliation(s)
- Kétyllen R Andrade
- Laboratório de Vírus, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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9
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Infection cycles of large DNA viruses: Emerging themes and underlying questions. Virology 2014; 466-467:3-14. [DOI: 10.1016/j.virol.2014.05.037] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 05/28/2014] [Accepted: 05/30/2014] [Indexed: 11/20/2022]
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10
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Yutin N, Wolf YI, Koonin EV. Origin of giant viruses from smaller DNA viruses not from a fourth domain of cellular life. Virology 2014; 466-467:38-52. [PMID: 25042053 DOI: 10.1016/j.virol.2014.06.032] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 06/14/2014] [Accepted: 06/21/2014] [Indexed: 11/27/2022]
Abstract
The numerous and diverse eukaryotic viruses with large double-stranded DNA genomes that at least partially reproduce in the cytoplasm of infected cells apparently evolved from a single virus ancestor. This major group of viruses is known as Nucleocytoplasmic Large DNA Viruses (NCLDV) or the proposed order Megavirales. Among the "Megavirales", there are three groups of giant viruses with genomes exceeding 500kb, namely Mimiviruses, Pithoviruses, and Pandoraviruses that hold the current record of viral genome size, about 2.5Mb. Phylogenetic analysis of conserved, ancestral NLCDV genes clearly shows that these three groups of giant viruses have three distinct origins within the "Megavirales". The Mimiviruses constitute a distinct family that is distantly related to Phycodnaviridae, Pandoraviruses originate from a common ancestor with Coccolithoviruses within the Phycodnaviridae family, and Pithoviruses are related to Iridoviridae and Marseilleviridae. Maximum likelihood reconstruction of gene gain and loss events during the evolution of the "Megavirales" indicates that each group of giant viruses evolved from viruses with substantially smaller and simpler gene repertoires. Initial phylogenetic analysis of universal genes, such as translation system components, encoded by some giant viruses, in particular Mimiviruses, has led to the hypothesis that giant viruses descend from a fourth, probably extinct domain of cellular life. The results of our comprehensive phylogenomic analysis of giant viruses refute the fourth domain hypothesis and instead indicate that the universal genes have been independently acquired by different giant viruses from their eukaryotic hosts.
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Affiliation(s)
- Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
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11
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Moelling K. What contemporary viruses tell us about evolution: a personal view. Arch Virol 2013; 158:1833-48. [PMID: 23568292 PMCID: PMC3755228 DOI: 10.1007/s00705-013-1679-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 02/14/2013] [Indexed: 12/11/2022]
Abstract
Recent advances in information about viruses have revealed novel and surprising properties such as viral sequences in the genomes of various organisms, unexpected amounts of viruses and phages in the biosphere, and the existence of giant viruses mimicking bacteria. Viruses helped in building genomes and are driving evolution. Viruses and bacteria belong to the human body and our environment as a well-balanced ecosystem. Only in unbalanced situations do viruses cause infectious diseases or cancer. In this article, I speculate about the role of viruses during evolution based on knowledge of contemporary viruses. Are viruses our oldest ancestors?
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Affiliation(s)
- Karin Moelling
- Max Planck Institute for Molecular Genetics, Ihnestr 63-73, 14195, Berlin, Germany.
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12
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Hingamp P, Grimsley N, Acinas SG, Clerissi C, Subirana L, Poulain J, Ferrera I, Sarmento H, Villar E, Lima-Mendez G, Faust K, Sunagawa S, Claverie JM, Moreau H, Desdevises Y, Bork P, Raes J, de Vargas C, Karsenti E, Kandels-Lewis S, Jaillon O, Not F, Pesant S, Wincker P, Ogata H. Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes. ISME JOURNAL 2013; 7:1678-95. [PMID: 23575371 PMCID: PMC3749498 DOI: 10.1038/ismej.2013.59] [Citation(s) in RCA: 155] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 02/28/2013] [Accepted: 03/06/2013] [Indexed: 11/17/2022]
Abstract
Nucleo-cytoplasmic large DNA viruses (NCLDVs) constitute a group of eukaryotic viruses that can have crucial ecological roles in the sea by accelerating the turnover of their unicellular hosts or by causing diseases in animals. To better characterize the diversity, abundance and biogeography of marine NCLDVs, we analyzed 17 metagenomes derived from microbial samples (0.2–1.6 μm size range) collected during the Tara Oceans Expedition. The sample set includes ecosystems under-represented in previous studies, such as the Arabian Sea oxygen minimum zone (OMZ) and Indian Ocean lagoons. By combining computationally derived relative abundance and direct prokaryote cell counts, the abundance of NCLDVs was found to be in the order of 104–105 genomes ml−1 for the samples from the photic zone and 102–103 genomes ml−1 for the OMZ. The Megaviridae and Phycodnaviridae dominated the NCLDV populations in the metagenomes, although most of the reads classified in these families showed large divergence from known viral genomes. Our taxon co-occurrence analysis revealed a potential association between viruses of the Megaviridae family and eukaryotes related to oomycetes. In support of this predicted association, we identified six cases of lateral gene transfer between Megaviridae and oomycetes. Our results suggest that marine NCLDVs probably outnumber eukaryotic organisms in the photic layer (per given water mass) and that metagenomic sequence analyses promise to shed new light on the biodiversity of marine viruses and their interactions with potential hosts.
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Affiliation(s)
- Pascal Hingamp
- CNRS, Aix-Marseille Université, Laboratoire Information Génomique et Structurale (UMR 7256), Mediterranean Institute of Microbiology (FR 3479), Marseille, France
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13
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Yutin N, Colson P, Raoult D, Koonin EV. Mimiviridae: clusters of orthologous genes, reconstruction of gene repertoire evolution and proposed expansion of the giant virus family. Virol J 2013; 10:106. [PMID: 23557328 PMCID: PMC3620924 DOI: 10.1186/1743-422x-10-106] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 03/27/2013] [Indexed: 12/01/2022] Open
Abstract
Background The family Mimiviridae belongs to the large monophyletic group of Nucleo-Cytoplasmic Large DNA Viruses (NCLDV; proposed order Megavirales) and encompasses giant viruses infecting amoeba and probably other unicellular eukaryotes. The recent discovery of the Cafeteria roenbergensis virus (CroV), a distant relative of the prototype mimiviruses, led to a substantial expansion of the genetic variance within the family Mimiviridae. In the light of these findings, a reassessment of the relationships between the mimiviruses and other NCLDV and reconstruction of the evolution of giant virus genomes emerge as interesting and timely goals. Results Database searches for the protein sequences encoded in the genomes of several viruses originally classified as members of the family Phycodnaviridae, in particular Organic Lake phycodnaviruses and Phaeocystis globosa viruses (OLPG), revealed a greater number of highly similar homologs in members of the Mimiviridae than in phycodnaviruses. We constructed a collection of 898 Clusters of Orthologous Genes for the putative expanded family Mimiviridae (MimiCOGs) and used these clusters for a comprehensive phylogenetic analysis of the genes that are conserved in most of the NCLDV. The topologies of the phylogenetic trees for these conserved viral genes strongly support the monophyly of the OLPG and the mimiviruses. The same tree topology was obtained by analysis of the phyletic patterns of conserved viral genes. We further employed the mimiCOGs to obtain a maximum likelihood reconstruction of the history of genes losses and gains among the giant viruses. The results reveal massive gene gain in the mimivirus branch and modest gene gain in the OLPG branch. Conclusions These phylogenomic results reported here suggest a substantial expansion of the family Mimiviridae. The proposed expanded family encompasses a greater diversity of viruses including a group of viruses with much smaller genomes than those of the original members of the Mimiviridae. If the OLPG group is included in an expanded family Mimiviridae, it becomes the only family of giant viruses currently shown to host virophages. The mimiCOGs are expected to become a key resource for phylogenomics of giant viruses.
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Affiliation(s)
- Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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14
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Clouthier SC, Vanwalleghem E, Copeland S, Klassen C, Hobbs G, Nielsen O, Anderson ED. A new species of nucleo-cytoplasmic large DNA virus (NCLDV) associated with mortalities in Manitoba lake sturgeon Acipenser fulvescens. DISEASES OF AQUATIC ORGANISMS 2013; 102:195-209. [PMID: 23446969 DOI: 10.3354/dao02548] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A newly discovered virus, Namao virus, associated with morbidity and mortality, was detected among juvenile lake sturgeon Acipenser fulvescens being propagated by a conservation stocking program for this endangered species in Manitoba, Canada. The outbreaks resulted in cumulative mortalities of 62 to 99.6% among progeny of wild Winnipeg River or Nelson River lake sturgeon and occurred at 2 geographically separate facilities. Namao virus was detected in almost 94% of the moribund or dead lake sturgeon according to a conventional polymerase chain reaction (cPCR) test that is based upon amplification of a 219 bp fragment of the virus major capsid protein (MCP). The virus itself was large (242 to 282 nm) and icosahedral-shaped with 2 capsids and a condensed bar-shaped core. It was found in virus factories within the host cell cytoplasm and displayed a tropism for the integument. Namao virus caused cellular changes characterized by enlarged eosinophilic epithelial cells in the gills and skin. Samples suspected of containing Namao virus did not have cytopathic effects on primary lake sturgeon or established white sturgeon cell lines. However, viral nucleic acid was detected in the former after prolonged incubation periods. Using primers designed from conserved regions of the MCP from NCLDVs, an estimated 95 to 96% of the Namao virus MCP open reading frame was captured. Phylogenetic analysis using the MCP of Namao virus and 27 other NCLDVs suggested that Namao virus and white sturgeon iridovirus share a common evolutionary past and might be members of the family Mimiviridae or a new, as yet unrecognized, virus family.
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Affiliation(s)
- Sharon C Clouthier
- Freshwater Institute, Fisheries & Oceans Canada, Winnipeg, Manitoba, Canada
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15
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Culley AI. Virophages to viromes: a report from the frontier of viral oceanography. Curr Opin Virol 2011; 1:52-7. [PMID: 22440567 DOI: 10.1016/j.coviro.2011.05.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Revised: 05/16/2011] [Accepted: 05/16/2011] [Indexed: 12/26/2022]
Abstract
The investigation of marine viruses has advanced our understanding of ecology, evolution, microbiology, oceanography and virology. Significant findings discussed in this review include the discovery of giant viruses that have genome sizes and metabolic capabilities that distort the line between virus and cell, viruses that participate in photosynthesis and apoptosis, the detection of communities of viruses of all genomic compositions and the preeminence of viruses in the evolution of marine microbes. Although we have made great progress, we have yet to synthesize the rich archive of viral genomic data with oceanographic processes. The development of cutting edge methods such as single virus genomics now provide a toolset to better integrate viruses into the ecology of the ocean.
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Affiliation(s)
- Alexander I Culley
- Center for Microbial Oceanography: Research and Education, Department of Oceanography, University of Hawaii at Manoa, CMORE Hale, Honolulu, HI 96822, United States.
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